In the series finale, [{Endgame}], the main starship classes from all three 24th century [Star Trek] spinoffs appear in the final shot of the episode. A Galaxy-class starship (the Enterprise-D from [Star Trek: The Next Generation]), a Defiant-class starship (the Defiant from [Star Trek: Deep Space Nine]), and of course an Intrepid-class starship (the Voyager from this series).

In the episode {Future's End} there is a gray figure on Rain Robinson's desk in the observatory. This figure is of a Talosian, who in the pilot episode of the original [Star Trek] series titled [{The Cage}] are the race that took Captain Christopher Pike captive.

The character of Tom Paris was a last-minute creation. Originally, Nicholas Locarno, (also played by Robert Duncan McNeill,) a Starfleet Academy cadet who had been expelled in the episode {The First Duty} of [Star Trek: The Next Generation], was to have been the person that Captain Janeway released from prison to help track down the Maquis ship. However, using Locarno in [Star Trek: Voyager] would have been problematic since Locarno had been drummed out of the academy with no possibility of ever joining Starfleet again. So they created Paris with a similar personality and backstory.